How to compare Neanderthal ancestry blocks between two sets of populations using SNP data

Question

[devenvyas]

I have SNP data on the Human Origins array. f4 and D statistics already tell me that these two regions have similar amounts of Neanderthal ancestry.

I want to determine whether the Neanderthal ancestry between the two regions comes from similar or different parts of the genome. I am not sure where precisely to start, and I was wondering if anyone has suggestions on where to start with this. Thanks!

Answer 1

[devenvyas]

Anyone have any ideas?